[gmx-users] gromacs 5.0 tools: gmx distance and gmx mindist time series

[Mark Abraham]

Hi

On Thu, May 7, 2015 at 3:34 PM oliwias <oliwias at ethz.ch> wrote:

> Hi Mark,
>
> I'm quite new to gromacs, so thanks for your help! I have an md
> trajectory in 3 files. I used:
> gmx_trjcat -f md1.xtc md2.xtc md3.xtc -o md.xtc -settime
> in order to get one file for analysis. I set the time of the first file
> to 0.0, and for the next two files I set the time to "c" (continue, I
> suppose). When I run:
> gmx check -f md.xtc -s1 md_2.tpr -c
> I get a message:
> "Timesteps at t=20000 don't match (2, 5)"
>
> I don't know why... The only reason that comes to my mind is that
> between run 1 and run 2 I changed the frequency of output.
>

Yes, that's what the message is telling you, in case you didn't know,
messed up, etc.


> Still, I don't understand why I get the time series when using the tool
> from gromacs 4.6 (seems that it doesn't care about the timestep
> mismatch), but not using gromacs 5.0?
>

Neither can we, since you didn't tell us what you did when you tried to get
the time series. Here you talked about how you built your inputs.

Mark


> Cheers,
> oliwia
>
>
> On 07.05.2015 14:59, Mark Abraham wrote:
> > Hi,
> >
> > Time series are what gmx distance does... see gmx distance -h, of
> > course.
> > If it's not working for you, you'll have to tell us exactly what you
> > tried,
> > what output you got, what's not suitable, etc., and check that your
> > input
> > files contain what you think they do (e.g. with gmx check)
> >
> > Mark
> >
> > On Thu, May 7, 2015 at 2:38 PM oliwias <oliwias at ethz.ch> wrote:
> >
> >> Dear All,
> >>
> >> I am trying to use the new gromacs 5.0 tools for analysis. I tried
> >> multiple options but I can't get gmx distance and gmx mindist to print
> >> out time series of distances. I only get the average. On the other
> >> hand,
> >> I had no problem with getting the time series with gromacs 4.6 g_dist
> >> and g_mindist. Don't know if it's a problem of the code or if I just
> >> don't know how to use the tool...
> >>
> >> I'd appreciate your tips!
> >> oliwia
> >> --
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